Members

Aleksei and his group are developing multi-resolution computational approaches to unravel physical principles that govern essential biological processes. In collaboration with the center’s experimentalists, they investigate how proteins and RNA diffuse through the cytoplasm, and how nuclear transport is enabled by the nuclear pore complex.

Mark and his team develop and validate novel computational methods for image analysis that will leverage MINFLUX and other data to advance the scientific mission of the center. They will also develop image formation methods that will enhance the capabilities of chemical imaging using infrared spectra, in collaboration with Bhargava and Zhang.

Mikael and his group will explore the theoretical and experimental limits of MINFLUX for biological microscopy tasks beyond single-particle localization, including orientation-dependent single particle imaging in live cells.

Stephen and his Biophotonics Imaging Laboratory team use novel label-free multi-modal nonlinear imaging methods to investigate mitochondrial and other organelle dynamics and distributions in living cells to understand the effect of stress on cells under varying metabolic states and stressors, working with Zhang and Bhargava to metabolite dynamics.

Glenn Fried and his colleagues at the IGB Core will be managing the MINFLUX microscope as well as adding AI tools for volume EM imaging and sequential FISH labeling. Glenn is also a main center contact with industry partner Abberior.

John and his JCVI team are experts in the culture, genetic manipulation, and biochemical analysis of the minimal bacterial cell they constructed, JCVI-syn3A. They will provide other QCB teams advice about working with those bacteria and as needed and will build and analyze minimal cell mutants to assist other QCB teams.

Ido and his lab illuminate the spatiotemporal dynamics of fundamental processes in bacterial cells using MINFLUX, single-molecule tracking (collaboration with Sangjin Kim), STORM and PAINT (collaboration with Paul Selvin). Ido also works with the Mehta group to characterize the transcriptional activity of individual cyanobacterial cells as they colonize a yeast host, en route to establishing endosymbiosis.

William will provide high performance computing expertise, particularly for parallel performance of applications and I/O, as well as providing access to the Delta and Delta AI supercomputers at NCSA, and massive data storage modalities needed for sharing and disseminating center data.

Taekjip’s team will use MINFLUX and multiplexed DNA-PAINT imaging in combination with genome-wide mapping of DNA mechanics and nucleosome condensation in collaboration with Prasanth and Aksimentiev to provide unique biophysical inputs to mesoscale modeling of chromosome organization and dynamics performed by Luthey-Schulten.

HyeonJun and his research team elucidate the underlying working mechanisms of DNA-binding proteins. They will enhance their research capabilities and provide critical data for whole cell models by utilizing MINFLUX to study how DNA-bound proteins behave on DNA under different experimental conditions.

Sangjin and her group will study the diffusion dynamics of macromolecules involved in gene expression in bacteria cells using MINFLUX, supporting one of the three cell types for which the center builds 4DWCMs.

Minjoung and her group will employ MINFLUX to investigate the internal structure of glucosomes, multienzyme condensates within human cells, across different cellular stress conditions and during the interactions with other cellular compartments.

Siewert-Jan and his group will perform coarse-grained simulations of cellsd to provide a dynamic cells at near-atomic resolution, to be linked with more coarse grained and whole cell models my machine-learning-based techniques.

Paola’s team will examine the dynamics of the bacterial chromosome at the initiation steps of chromosome replication and segregation using the MINFLUX system and work with the Luthey-Schulten and Kim teams to model centromere segregation in bacteria.

Eric will coordinate science communication activities and research including facilitation of trainings and workshops for faculty and students associated with the center, offering a graduate level class in communicating science, and developing a formal certificate in science communication for the center that will provide opportunities for individuals beyond the university.

Kannanganattu’s laboratory will use the MINFLUX microscope to quantify the dynamic interactions of nuclear domain-resident RNA binding proteins during various cellular stresses in eukaryotic cells, complementing investigations such as Gruebele’s MINFLUX-spliceosome studies.

Lei and his group will use machine learning techniques to study protein function in cells. He is also in charge of the program outreach effort for the center at Fisk University.

Luisa and the I-STEM evaluation team will monitor, document and report on the implementation, effectiveness, impact, and institutionalization of the STC-QCB’s research, outreach and educational activities and guide the Center via understanding and improvement of “program theory.”

Paul and his group will use the MINFLUX to detect fast “half-steps” of kinesin and dynein in three dimensions and as a function of force, as well as develop magnetic bead force measurements for MINFLUX.

Emad’s group develops and applies molecular modeling, simulation, and visualization to the investigation of dynamics-function relationships in biomolecular systems and processes. They recently moved into the challenging area of cell-scale modeling and simulation, focusing mostly on membrane assemblies, such as the viral envelopes and capsids. A recent key collaboration between Emad and Martin focused on the stability of the capsid in Hepatitis B virus.

Shuleiand his group are developing machine learning methods and advanced statistical computational tools for large and complex biological data sets, including multi-omics and imaging data, like MINFLUX, used by Gruebele, Backlund and others to maximize data extraction.

Kai and his lab use MINFLUX super-resolution imaging to investigate the assembly of supramolecular complex such as virus-like particles and inflammasomes, as well as dynamic interactions between organelles in cells.

Yingjie and his group will develop a new infrared tomography system for 3-D chemical profiling of metabolites in live cells with sub-cellular resolution. This work is done in close collaboration with the Bhargava group among others.